Table 1.
Confirmed common variant susceptibility regions identified for epithelial ovarian cancer, by subtype, and annotated for regulatory biofeatures identified in ovarian cancer precursor tissues
| Locus | Subtypea | Top SNP | Mapped window (kb) | Number 1:100 SNPs | OR (95%CI) | P-value¶ | Nearest gene | Number predicted TF motifs | Motifs |
|---|---|---|---|---|---|---|---|---|---|
| 1p36.12 | Invasive | rs56318008 | 152 | 34 | 1.11 (1.07–1.16) | 7.6 × 10−9 | WNT4 | 9 | CTCF, TCF12, ZEB1, MEF2, RFX5, HSF1, TAL1, RUNX1, ETS1, TEAD1, CREB, SREBF1, CEBPB |
| 1p34.3 | HGSOC | rs58722170 | 33 | 14 | 1.08 (1.04–1.12) | 2.7 × 10−12 | RSPO1 | NA | NA |
| 2q31 | HGSOC | rs2072590 | 22 | 16 | 1.14 (1.10–1.19) | 3.7 × 10−13 | HOXD | 7 | AP2, UA3, UA12, UA3, UA8, ZEB1, UA9, BARHL2, UA8, EBF1, RUNX1 |
| 3q25 | HGSOC | rs7651446 | 176 | 63 | 1.59 (1.48–1.70) | 1.5 × 10−38 | TiPARP | 30 | — |
| 4q26 | Invasive | rs17329882 | 13 | 3 | 1.09 (1.06–1.13) | 1.4 × 10−8 | SYNPO2 | 2 | AP1, BARHL2, UA8, BARHL2, CEBPB, ETS1 |
| 5p15.15 | HGSOC | rs10069690 | 5 | 8 | 1.14 (1.10–1.19) | 7.6 × 10−11 | TERT | 0 | NA |
| 6p22.1 | HGSOC | rs1161331104 | 91 | 17 | 0.93 (0.91–0.97) | 3.0 × 10−8 | GPX6 | NA | NA |
| 8q21 | HGSOC | rs11782652 | 60 | 9 | 1.24 (1.16–1.32) | 5.6 × 10−11 | CHMP4C | 1 | BARHL2, PRDM1, SOX2 |
| 8q24 | HGSOC | rs10088218 | 32 | 49 | 0.77 (0.73–0.82) | 1.6 × 10−20 | MYC/ PVT1 | 19 | — |
| CCOC | rs2165805 | 18 | 2 | 1.21 (1.05–1.40) | 8.4 × 10−9 | NA | NA | ||
| 9p22 | HGSOC | rs3814113 | 10 | 17 | 0.79 (0.76–0.82) | 2.7 × 10−34 | BNC2 | 1 | TAL1 |
| 9q34.2 | Invasive | rs635634 | 224 | 15 | 1.11 (1.07–1.16) | 4.4 × 10−9 | ABO | 0 | NA |
| 10p12 | HGSOC | rs1243180 | 210 | 48 | 1.10 (1.06–1.14) | 1.2 × 10−9 | MLLT10 | 12 | |
| 17q11.2 | Invasive | chr17:29181220:I5 | 270 | 17 | 0.91 (0.88–0.94) | 2.6 × 10−9 | ATAD5 | 0 | NA |
| 17q12 | CCOC | rs11651755 | 14 | 16 | 0.80 (0.72–0.88) | 2.9 × 10−8 | HNF1B | 4 | YY1, CTCF, ETS1, ETS1 |
| HGSOC | rs757210 | 16 | 9 | 1.11 (1.07–1.15) | 8.2 × 10−9 | 1 | ETS1 | ||
| 17q21.31 | HGSOC | rs183211 | 113 | 148 | 1.11 (1.07–1.16) | 1.6 × 10−7 | PLEKHM1 | 30 | |
| 17q21.32 | HGSOC | rs9303542 | 162 | 95 | 1.14 (1.10–1.19) | 4.0 × 10−12 | SKAP1 | 8 | SOX2, TEAD1, ELF1, ELK4, ETS1, GABP, BHLHE40, MYC, AP2, UA3, UA8, SOX2, TAL1, TBP, TCF7L2, ETS1, RUNX1, SOX2, TCF12, UA9, ZEB1, SOX2 |
| 19p13 | HGSOC | rs4808075 | 20 | 13 | 1.18 (1.13–1.23) | 2.9 × 10−14 | ANKLE1 | 2 | ELF1, ELK4, GABP, GATA3 |
aHigh-grade serous ovarian cancer (HGSOC); ovarian clear cell cancer (OCCC); All invasive ovarian cancer subtypes combined (Invasive).
¶P-value for the strongest association listed by subtype. Where all invasive ovarian cancers gave the strongest P-value, the association for HGSOC was the subtypes with the strongest effect with the following P-values: 5.7 × 10−8 at 1p36.12, 1.6 × 10−8 at 4p26, 4.2 × 10−8 at 9q34.2 and 3.9 × 10−7 at 17q11.2.